When I first played .flow I could have sworn that Sabitsuki was male. So it may sound like a stupid question, but what makes us sure Sabitsuki is female, and not just a male with gender issues due to the male qualities they exhibit.

We don't actually as far as I know. Do keep in mind I haven't seen the designers art but there is a theory that she/he is transgender. It could be possible that she/he is male. I don't personally think so but it could be.